*Target (protein/gene name): fabH 3-oxoacyl-[acyl-carrier-protein] synthase 3 *NCBI Gene # or RefSeq#: 8333 *Protein ID (NP or XP #) or Wolbachia#: NP_415609.1. *Organism (including strain):Escherichia coli (strain K12) */Disease Information (sort of like the Intro to your Mini Research Write up): Francisella tularensis is pathogenic bacterial species that is the causing agent of tularemia, which is lethal without treatment. F. tularensis is classified as a Tier 1 select agent by the U.S. government due to its low infectious dose, aerosol dispersion potential, and high virulence. Link to TDR Targets page (if present): Link to Gene Database page (NCBI, EuPath databases -e.g. TryTryp, PlasmoDB, etc - or PATRIC, etc.) https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?lvl=0&id=83333 Essentiality of this protein: Gene/Ortholog: mtu541 (OG4_12762); Phenotype: non-essential; Source study: nmpdr Gene/Ortholog: eco1055 (OG4_12762); Phenotype: undefined; Source study: blattner Gene/Ortholog: eco1055 (OG4_12762); Phenotype: essential; Source study: gerdes Gene/Ortholog: eco1055 (OG4_12762); Phenotype: non-essential; Source study: keio Gene/Ortholog: eco1055 (OG4_12762); Phenotype: non-essential; Source study: shigen Is it a monomer or multimer as biological unit? (make prediction athttp://www.ebi.ac.uk/msd-srv/prot_int/pistart.html): multimer Complex of proteins?: No Druggable Target (list number or cite evidence from a paper/database showing druggable in another organism): Druggability index (range: 0 to 1): 0.3
acetyl-CoA + a malonyl-[acyl-carrier protein] = an acetoacetyl-[acyl-carrier protein] + CoA + CO2
Enzyme Assay information (spectrophotometric, coupled assay ?, reagents): -- -or link (or citation) to paper that contains assay information
Structure (PDB or Homology model) -- PDB # or closest PDB entry if using homology model: ----- 1EBL What is the PDB identifier - Dr. B
Figure 1: PDB entry for fabH 3-oxoacyl-[acyl-carrier-protein] synthase 3
Current Inhibitors: Inhibited by the SB418011 antibiotic. Not inhibited by cerulenin and thiolactomycin. Expression Information (has it been expressed in bacterial cells): N/A Purification Method:
immobilized metal ion affinity chromatography (Ni2+)
- 719087, 719093
recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography and dialysis
- 736053
recombinant His-tagged enzyme from strain BL21(DE3)
- 665468
recombinant His-tagged wild-type and mutant enzymes from strain BL21(DE3)
- 666950
recombinant native and selenomethionine-labeled enzyme from Escherichia coli strain DH10B to homogeneity by two different steps of anion exchange and a step of hydroxyapatite chromatography
- 702661
recombinant selenomethionine-labeled enzyme by ion exchange, hydroxylapatite, and affinity chromatography, and gel filtration
- 663822
to homogeneity in three chromatographic steps (Q-Sepharose, MonoQ, and hydroxyapatite)
- 719085
to homogeneity in three chromatographic steps (Q-Sepharose, MonoQ, and hydroxyapatite), immobilized metal ion affinity chromatography (Ni2+)
*length of your protein in Amino Acids: 317 Molecular Weight of your protein in kiloDaltons using the Expasy ProtParam website: 33515.12 Molar Extinction coefficient of your protein at 280 nm wavelength: 25690 TMpred graph Image (http://www.ch.embnet.org/software/TMPRED_form.html). Input your amino acid sequence to it.
results
*CDS Gene Sequence (paste as text only): NC_000913.3
*GC% Content for gene: *CDS Gene Sequence (codon optimized) - copy from output of Primer Design Protocol (paste as text only): *GC% Content for gene (codon optimized):
Do Not Need this info for Spring (but still copy these lines to your Target page for now) Primer design results for pNIC-Bsa4 cloning (list seqeunces of all of your ~40 nt long primers): (link to DNA Works output text file - that should be saved in your Google Docs folder after you did the primer design protocol) -- Ask a mentor, Dr. B, or a fellow researcher -how to link a GDocs file if you are not sure how to.
Primer design results for 'tail' primers (this is just 2 sequences): **
*NCBI Gene # or RefSeq#: 8333
*Protein ID (NP or XP #) or Wolbachia#: NP_415609.1.
*Organism (including strain): Escherichia coli (strain K12)
*/Disease Information (sort of like the Intro to your Mini Research Write up): Francisella tularensis is pathogenic bacterial species that is the causing agent of tularemia, which is lethal without treatment. F. tularensis is classified as a Tier 1 select agent by the U.S. government due to its low infectious dose, aerosol dispersion potential, and high virulence.
Link to TDR Targets page (if present):
Link to Gene Database page (NCBI, EuPath databases -e.g. TryTryp, PlasmoDB, etc - or PATRIC, etc.)
https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?lvl=0&id=83333
Essentiality of this protein:
Gene/Ortholog: mtu541 (OG4_12762); Phenotype: non-essential; Source study: nmpdr
Gene/Ortholog: eco1055 (OG4_12762); Phenotype: undefined; Source study: blattner
Gene/Ortholog: eco1055 (OG4_12762); Phenotype: essential; Source study: gerdes
Gene/Ortholog: eco1055 (OG4_12762); Phenotype: non-essential; Source study: keio
Gene/Ortholog: eco1055 (OG4_12762); Phenotype: non-essential; Source study: shigen
Is it a monomer or multimer as biological unit? (make prediction at http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html): multimer
Complex of proteins?: No
Druggable Target (list number or cite evidence from a paper/database showing druggable in another organism):
Druggability index (range: 0 to 1): 0.3
2 chemical compounds are associated with this gene
- Predicted associations
- By orthology to known druggable targets
From ChEMBL- || Mycobacterium tuberculosis || 3-oxoacyl-[acyl-carrier-protein] synthase III || Show papers || show compounds ||
- || Haemophilus influenzae || Beta-ketoacyl-ACP synthase III || Show papers || show compounds ||
- || Streptococcus pyogenes serotype M3 || Beta-ketoacyl-ACP synthase III || Show papers || show compounds ||
- || Staphylococcus aureus subsp. aureus Mu50 || Beta-ketoacyl-ACP synthase III || Show papers || show compounds ||
- || Enterococcus faecalis || Beta-ketoacyl-ACP synthase III || Show papers || show compounds ||
- || Plasmodium falciparum 3D7 || Beta-ketoacyl-ACP-synthase III || Show papers || show compounds ||
- || Escherichia coli || 3-oxoacyl-[acyl-carrier-protein] synthase 3 || Show papers || show compounds ||
From TDR Targets*EC#: 2.3.1.180
Link to BRENDA EC# page: http://www.brenda-enzymes.org/enzyme.php?ecno=2.3.1.180&UniProtAcc=P0A6R0&OrganismID=2026
-- Show screenshot of BRENDA enzyme mechanism schematic
acetyl-CoA + a malonyl-[acyl-carrier protein] = an acetoacetyl-[acyl-carrier protein] + CoA + CO2
Enzyme Assay information (spectrophotometric, coupled assay ?, reagents):
-- -or link (or citation) to paper that contains assay information
Structure (PDB or Homology model)
-- PDB # or closest PDB entry if using homology model: ----- 1EBL What is the PDB identifier - Dr. B
Current Inhibitors:
Inhibited by the SB418011 antibiotic. Not inhibited by cerulenin and thiolactomycin.
Expression Information (has it been expressed in bacterial cells): N/A
Purification Method:
immobilized metal ion affinity chromatography (Ni2+)
-
719087, 719093
recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography and dialysis
-
736053
recombinant His-tagged enzyme from strain BL21(DE3)
-
665468
recombinant His-tagged wild-type and mutant enzymes from strain BL21(DE3)
-
666950
recombinant native and selenomethionine-labeled enzyme from Escherichia coli strain DH10B to homogeneity by two different steps of anion exchange and a step of hydroxyapatite chromatography
-
702661
recombinant selenomethionine-labeled enzyme by ion exchange, hydroxylapatite, and affinity chromatography, and gel filtration
-
663822
to homogeneity in three chromatographic steps (Q-Sepharose, MonoQ, and hydroxyapatite)
-
719085
to homogeneity in three chromatographic steps (Q-Sepharose, MonoQ, and hydroxyapatite), immobilized metal ion affinity chromatography (Ni2+)
-
719068, 719086
*Amino Acid Sequence (paste as text only - not as screenshot or as 'code'):
<span style="color: #222222; font-family: monospace,monospace; font-size: 14.04px;"> 10 20 30 40 50 MYTKIIGTGS YLPEQVRTNA DLEKMVDTSD EWIVTRTGIR ERHIAAPNET 60 70 80 90 100 VSTMGFEAAT RAIEMAGIEK DQIGLIVVAT TSATHAFPSA ACQIQSMLGI 110 120 130 140 150 KGCPAFDVAA ACAGFTYALS VADQYVKSGA VKYALVVGSD VLARTCDPTD 160 170 180 190 200 RGTIIIFGDG AGAAVLAASE EPGIISTHLH ADGSYGELLT LPNADRVNPE 210 220 230 240 250 NSIHLTMAGN EVFKVAVTEL AHIVDETLAA NNLDRSQLDW LVPHQANLRI 260 270 280 290 300 ISATAKKLGM SMDNVVVTLD RHGNTSAASV PCALDEAVRD GRIKPGQLVL 310 LEAFGGGFTW GSALVRF </span>*length of your protein in Amino Acids: 317Molecular Weight of your protein in kiloDaltons using the Expasy ProtParam website: 33515.12
Molar Extinction coefficient of your protein at 280 nm wavelength: 25690
TMpred graph Image (http://www.ch.embnet.org/software/TMPRED_form.html). Input your amino acid sequence to it.
*CDS Gene Sequence (paste as text only): NC_000913.3
*GC% Content for gene:
*CDS Gene Sequence (codon optimized) - copy from output of Primer Design Protocol (paste as text only):
*GC% Content for gene (codon optimized):
Do Not Need this info for Spring (but still copy these lines to your Target page for now)
Primer design results for pNIC-Bsa4 cloning (list seqeunces of all of your ~40 nt long primers):
(link to DNA Works output text file - that should be saved in your Google Docs folder after you did the primer design protocol)
-- Ask a mentor, Dr. B, or a fellow researcher -how to link a GDocs file if you are not sure how to.
Primer design results for 'tail' primers (this is just 2 sequences):
**